I'm trying to create a new project and running into trouble combining the App Engine Standard project type with Gradle. I've tried creating a Gradle project and adding App Engine Standard to it, and I've tried creating an App Engine Standard project and adding Gradle to it. Neither have yielded a working result. I'm sure it is a matter of not knowing the correct sequence of actions to take and / or choices to make in the dialogs, but the documentation doesn't address this combination well. The documentation doesn't describe how to start a new project through IDEA, it simply points at a GitHub repo as an example of a finished product.
How to create a new project using both App Engine Standard (Java 8) and Gradle
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The IDEA Cloud Tools plugin supports new project generation but only for native IntelliJ projects and doesn't generate a build.gradle for you.
I wouldn't recommend it as a starting point for a gradle based project anyway due to its directory structure.
IMO using the starter project on Github from the documentation you mentioned is the best approach to start. You can clone it, delete the .git directory and import that into IntelliJ and should have a decent starting point for your project.